Classification of gliomas based on genome-wide DNA methylation profiles and immunohistochemical analysis: a short study.

in Folia neuropathologica by Olga Taryma-Leśniak, Kamil Buczkowski, Tomasz Klepinowski, Maciej Jankowski, Szymon Retfiński, Bartłomiej Sagan, Leszek Sagan, Ewa Szutowicz, Kacper Winiarski, Marta Masztalewicz, Przemysław Nowacki, Marta Sobalska-Kwapis, Dominik Strapagiel, Wojciech Kloc, Beata Lipska-Ziętkiewicz, Ewa Iżycka-Świeszewska, Tomasz K Wojdacz

TLDR

  • The study demonstrates the efficacy of methylation analysis for diagnosing diffuse gliomas using Infinium Methylation-EPIC microarrays, but highlights the limitations of the method and the importance of combined pathological and clinical analysis.

Abstract

Methylation profiling is one of the diagnostic methods included in the 2021 World Health Organization Classification of Central Nervous System Tumors (WHO CNS5). In the present short study, we performed methylation analysis of 16 archival diffuse gliomas, including seven glioblastomas (GB) with long survival and three GB with early disease presentation. The formalin-fixed paraffin-embedded (FFPE) and freshly frozen (FF) samples were analyzed using Infinium Methylation-EPIC microarrays. The diagnosis was changed in two cases, and two other cases were classified as control tissue due to the low content of neoplastic cells in examined frozen samples. No differences were found between the usefulness of FF and FFPE material for methylation profiling. Copy number variation analysis and comparative immunohistochemical and molecular studies were also performed. The MGMT promoter methylation assessment was consistent between the micro-array and methylation-sensitive high-resolution melting (MS-HRM) testing. The performed analyses did not supply new data according to the unexpected clinical course of the selected cases. Immunohistochemical evaluation with p16 and PTEN antibodies was consistent with the CDKN2A and PTEN status in most cases. In conclusion, the classification of gliomas based on genome-wide methylation profiles increases the precision of histopathological diagnosis but has limitations, and pathological and clinical consistency is always necessary. Furthermore, immunohistochemical surrogates of molecular alterations are suitable and widely available diagnostic tools.

Overview

  • The study aimed to investigate the efficacy of methylation analysis for diagnosing diffuse gliomas using Infinium Methylation-EPIC microarrays.
  • Methylation analysis was performed on 16 archival diffuse gliomas, including 7 glioblastomas with long survival and 3 GB with early disease presentation.
  • The study compared the usefulness of using formalin-fixed paraffin-embedded (FFPE) and freshly frozen (FF) samples for methylation profiling.

Comparative Analysis & Findings

  • No differences were found between the usefulness of FF and FFPE material for methylation profiling.
  • The diagnosis was changed in two cases, and two other cases were classified as control tissue due to the low content of neoplastic cells in examined frozen samples.
  • The MGMT promoter methylation assessment was consistent between the micro-array and methylation-sensitive high-resolution melting (MS-HRM) testing.

Implications and Future Directions

  • The classification of gliomas based on genome-wide methylation profiles increases the precision of histopathological diagnosis.
  • However, the study highlights the limitations of methylation analysis and the importance of pathological and clinical consistency.
  • Immunohistochemical surrogates of molecular alterations are suitable and widely available diagnostic tools for glioma diagnosis.
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